Proteopedia:Policy

Links to Wikipedia
Do not link to Wikipedia (or to any external site) from the main body of a Proteopedia page. You may place a link to the Wikipedia page that deals with the same topic as that Proteopedia page at the bottom of that Proteopedia page in a section called "External Resources". Make "External Resources" the last section in the page, right after the "References" section.

Additional Explanation about Links to Wikipedia

 * 1) Most topics should have their own page in Proteopedia, even if initially that page contains nothing but a link to the corresponding page on the topic in Wikipedia
 * 2) If the page exists within Proteopedia, you should link to it, and not to Wikipedia.
 * 3) If the page topic is a protein or a molecule, especially one that could benefit from Jmol applets and scenes to describe it structurally, then a "red" link to an empty page in Proteopedia might encourage someone to create the page within Proteopedia, and should be created.
 * 4) The name of a crystallographer should link within Proteopedia and that page may contain a link to her/his entry in Wikipedia if it exists.
 * 5) When Wikipedia has an article relevant to Proteopedia, one should never hesitate to link to Wikipedia. However, such links to Wikipedia should nearly always be made on a page with the same topic in Proteopedia. There is no reason to duplicate what is in Wikipedia within Proteopedia. However, often Proteopedia may wish to emphasize or summarize specific aspects of a topic, whereas Wikipedia will attempt to be broad and comprehensive. That is the reason for the following rule.
 * 6) For most topics, and certainly when in doubt, it is better to create a new page within Proteopedia, and then put a link to Wikipedia on that Proteopedia page on the same topic. This provides a place to emphasize aspects of the topic important to Proteopedia, even though these aspects may be mentioned somewhere in Wikipedia's article. For example, the Proteopedia page on the Protein Data Bank could emphasize that new entries are released weekly, and that following each weekly release, new Proteopedia pages are created for each new entry automatically, a process called "seeding". However, the Proteopedia page on the Protein Data Bank need not repeat everything that Wikipedia says, and should certainly link to the Wikipedia article for more information. Also, we don't want to scatter links to Wikipedia's articles throughout Proteopedia articles, and then later realize it would have been better to have all those links go to to a Proteopedia article (which in turn links to Wikipedia). This would probably create a maintenance problem, trying to find and update all those links.
 * 7) If the page is unrelated to proteins or molecules (like a page for an organism), and the page exists and is useful within Wikipedia, you may link directly to Wikipedia, but ideally not within the main body of the Proteopedia page (See the external links section of this page)
 * 8) A link to Wikipedia should be inserted as

Make New Topic Pages and Avoid Editing the Pages Titled with PDB Codes
Please make Topic pages if there is not yet one for your topic of interest. Pages titled with a PDB identification code are initially created automatically ( ' seeded ' ), and include the Publication Abstract from PubMed copied from the paper reporting the PDB entry. These seeded pages have a standardized format and we prefer it remain relatively constant so that they feature the pertinent information. However, topic pages are less constrained. You may wish to begin by filling your topic page with the seeded page from a related structure. A topic page can be manually-created content. If you do write a better overview, feature it on the topic page and do not feel that the corresponding abstract(s) must remain. The abstract should remain on the seeded page though. We prefer you do your editing on topic pages and link to the appropriate seeded pages. Also, link the seeded page with the concerned PDB codes to your topic page; this is the exception for which we do encourage editing of the seeded pages. Your topic pages should feature prominently information important for non-specialists trying to understand the structure and function of the concerned macromolecules and these should be illustrated with molecular scenes which make Proteopedia unique from other wikis. If you have detailed information concerning the topic or structure, please place it in the page towards the bottom or make a separate page related to the more general topic.

Avoid Obscure Page Titles
Please avoid using titles for new Topic pages that will not be meaningful to non-specialists. For example, titles that are specialist acronyms such as SGAP, Cyt2Ba, Nqo1, and VirE1/VirE2 will not be meaningful to most users of Proteopedia. Using the move tab, these pages have been retitled. When a page is moved (renamed), a redirect page is automatically created from the old title -- therefore searching for the old title will still find the page with the new title. That is why clicking a link such as SGAP goes to the longer and more generally meaningful title. You will see that there is a note, just below the title, that you have been redirected.

Please Don't Delete Abstracts or Edit Extensively on the Pages Titled with PDB Codes
Pages titled with a PDB identification code are initially created automatically ( ' seeded ' ), and include the Publication Abstract from PubMed copied from the paper reporting the PDB entry. Even if you write a better overview of the paper or the structure, please do not remove the published abstract. However, you should not be editing the pages titled with a PDB identification code anyway. We prefer you do your editing on topic pages and link to the appropriate seeded pages. Also, link the seeded page with the concerned PDB codes to your topic page; this is the exception for which we do encourage editing of the seeded pages. If you do write a better overview, feature it prominently on the topic page and do not feel you need to have the corresponding abstract(s).

Protected Pages
Any registered user (after logging in) can create protected pages. How? Please see Help:Protected_Pages. Protecting a page means that its author does not have to worry about the content being changed by someone else. However, all content in Proteopedia is freely available to be copied, edited, used and adapted (click on the GNU Free Document License icon at the lower left of the page for details). Therefore, anyone may copy the content of a protected page into a publicly editable page, where it can evolve in true wiki fashion. Equally, you may copy it into your own protected page, where you may edit it to fit your needs. Examples:
 * User:Eric_Martz/Nucleosomes is a protected page. Only its author is able to edit it.
 * Nucleosomes contains a copy of the content in the above page, plus other material. Any logged-in user can edit this page.

PDB Code in Plain Sight
Please make sure that every page shows, in plain sight, the PDB code(s) for the atomic coordinates used in the molecular scenes shown on that page. The standard place to put the PDB code is beneath the molecular scene in the caption to Jmol. If one Jmol is used to show more than one PDB entry, only then should the PDB codes be moved to the text (near the first green links that show them). If you modify the PDB file, it is still important to state the code -- please see the next section.

Altered PDB Files
Any PDB file that has been modified and uploaded to Proteopedia must be noted as such and the modifications explained, preferably in the summary section when uploading the file, as well as in the page where the modified PDB file appears. If you prefer to make the note explaining the modifications less obtrusive, it can be in a reference footnote.

Theoretical Models
In the broad sense intended here, theoretical model means any molecular model that is not derived directly from empirical atomic resolution data, such as crystallographic X-ray diffraction, or a sufficient number of NMR restraints. "Theoretical model" thus includes comparative or homology models, ab initio / de novo models, or any modification to an empirical model, including changes as small as the mutation of a single amino acid.

The positions of sidechains in theoretical models, such as comparative models, or models with theoretically added mutations or changes in conformation, are generally unreliable. The backbone conformation or fold is generally unreliable in ab initio / de novo theoretical models.

1,390 theoretical models were historically deposited in the Protein Data Bank but removed from the main database in 2002. Pages automatically generated in Proteopedia for these theoretical models do not display these structures due to their unreliability (see Category:Theoretical Model).

Proteopedia users are free to display an uploaded theoretical model, provided that it is clearly identified. Methods recommended for such identification are explained at Proteopedia:Cookbook.

Examples

 * The article Structure of E. coli DnaC helicase loader is about a homology model.
 * A theoretical model can be displayed from a green link on the page for the empirical model 1vzj.

Main Page
The Main Page of Proteopedia must be kept concise and minimalistic. However, a user should be able to answer any of their questions by following no more than two links starting from the Main Page. It should be obvious to the user which links to follow to arrive at the answer to his or her question. For example, a user looking for a detailed description of how to use the Scene Authoring Tools would first click on the "editing-help page" link from the "Want to Contribute" section on the Main Page, and on the "editing-help page", quickly find a link through the table of contents to the Scene Authoring Tools help page.

Page Contributors and, Editors vs. Content Donators
Please see Proteopedia Page Contributors and Editors.